Merge pull request #726 from suny-downstate-medical-center/release/1.…

…0.3.1

PR from release/1.0.3.1 to master - VERSION 1.0.3.1

CHANGES.md

@@ -1,3 +1,7 @@
+# Version 1.0.3.1
+
+- Hotfix to support new GUI functionality
+
 # Version 1.0.3
 
 **New features**

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.3'
+version = '1.0.3.1'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.3'
+release = '1.0.3.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

netpyne/__init__.py

@@ -4,7 +4,7 @@
 NetPyNE consists of a number of sub-packages and modules.
 """
 
-__version__ = '1.0.3'
+__version__ = '1.0.3.1'
 import os, sys
 display = os.getenv('DISPLAY')
 nogui = (sys.argv.count('-nogui')>0)

netpyne/batch/batch.py

@@ -22,16 +22,8 @@
 except NameError:
     to_unicode = str
 
-import imp
-import json
-import pickle
-import logging
 import datetime
-from copy import copy
-from random import Random
-from time import sleep, time
-from itertools import product
-from subprocess import Popen, PIPE
+from time import time
 import importlib, types
 
 from neuron import h
@@ -42,21 +34,6 @@
 from .evol import evolOptim
 from .asd_parallel import asdOptim
 
-try:
-    from .optuna_parallel import optunaOptim
-except:
-    pass
-    # print('Warning: Could not import "optuna" package...')
-
-
-try:
-    from .sbi_parallel import sbiOptim
-except:
-    pass
-    #print('Error @ the batch.py file import section')
-
-
-
 
 pc = h.ParallelContext() # use bulletin board master/slave
 if pc.id()==0: pc.master_works_on_jobs(0)
@@ -277,6 +254,7 @@ def run(self):
         # -------------------------------------------------------------------------------
         elif self.method == 'optuna':
             try:
+                from .optuna_parallel import optunaOptim
                 optunaOptim(self, pc)
             except Exception as e:
                 import traceback
@@ -288,6 +266,7 @@ def run(self):
         # -------------------------------------------------------------------------------
         elif self.method == 'sbi':
             try:
+                from .sbi_parallel import sbiOptim
                 sbiOptim(self, pc)
             except Exception as e:
                 import traceback

netpyne/batch/grid.py

@@ -185,40 +185,6 @@ def gridSearch(batch, pc):
     if batch.runCfg.get('type',None) == 'mpi_bulletin':
         pc.runworker() # only 1 runworker needed in rank0
 
-    createFolder(batch.saveFolder)
-
-    # save Batch dict as json
-    targetFile = batch.saveFolder+'/'+batch.batchLabel+'_batch.json'
-    batch.save(targetFile)
-
-    # copy this batch script to folder
-    targetFile = batch.saveFolder+'/'+batch.batchLabel+'_batchScript.py'
-    os.system('cp ' + os.path.realpath(__file__) + ' ' + targetFile)
-
-    # copy netParams source to folder
-    netParamsSavePath = batch.saveFolder+'/'+batch.batchLabel+'_netParams.py'
-    os.system('cp ' + batch.netParamsFile + ' ' + netParamsSavePath)
-
-    # import cfg
-    if batch.cfg is None:
-        cfgModuleName = os.path.basename(batch.cfgFile).split('.')[0]
-
-        try:
-            loader = importlib.machinery.SourceFileLoader(cfgModuleName, batch.cfgFile)
-            cfgModule = types.ModuleType(loader.name)
-            loader.exec_module(cfgModule)
-        except:
-            cfgModule = imp.load_source(cfgModuleName, batch.cfgFile)
-
-        batch.cfg = cfgModule.cfg
-
-    batch.cfg.checkErrors = False  # avoid error checking during batch
-
-    # set initial cfg initCfg
-    if len(batch.initCfg) > 0:
-        for paramLabel, paramVal in batch.initCfg.items():
-            batch.setCfgNestedParam(paramLabel, paramVal)
-
     processes, processFiles = [],[]
 
     if batch.method == 'list':
@@ -280,7 +246,9 @@ def gridSearch(batch, pc):
         except:
             pass
     pc.done()
-    h.quit()
+    # TODO: line below was commented out due to issue on Netpyne-UI (https://dura-bernallab.slack.com/archives/C02UT6WECEL/p1671724489096569?thread_ts=1671646899.368969&cid=C02UT6WECEL)
+    # Needs to be re-visited.
+    # h.quit()
 
 def gridSubmit(batch, pc, netParamsSavePath, jobName, simLabel, processes, processFiles):